Cited by Epistasis and cryptic QTL identified using modified bulk segregant analysis of copper resistance in budding yeast

The effects of loss of Y chromosome on male health DOI

Bożena Bruhn‐Olszewska,

Ellen Markljung,

Edyta Rychlicka-Buniowska

et al.

Nature Reviews Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

Language: Английский

Citations

Human embryo editing against disease is unsafe and unproven — despite rosy predictions DOI

Shai Carmi, Henry T. Greely,

Kevin J. Mitchell

et al.

Nature, Journal Year: 2025, Volume and Issue: 637(8046), P. 554 - 556

Published: Jan. 8, 2025

Language: Английский

Citations

An initial exploration of core collection construction and DNA fingerprinting in Elymus sibiricus L. using SNP markers DOI

Xinrui Li, Daniel Y. Song, Mingfeng Li

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 7, 2025

Elymus sibiricus L., an excellent forage and ecological restoration grass, plays a key role in grassland construction the sustainable development of animal husbandry. In China, wild germplasm resources E. are abundant, they shaped by similar contrasting climatic conditions to form distinct populations, which enrich genetic diversity sibiricus. To more comprehensively aggregate at lower cost accurately utilize its variation, this study conducted preliminary exploration core collections fingerprinting using single nucleotide polymorphism (SNP) markers. By combining multiple evaluation measures with weighted processing, we successfully identified 36 materials from 90 samples serve as collection. Genetic assessments, allele evaluations, principal component analyses all indicate that these represent accessions. Additionally, 290 SNP loci among high-quality generated whole-genome sequencing candidate Of these, 52 were selected markers for DNA Using kompetitive allele-specific PCR (KASP) technology, also performed population origin identification 60 accessions based on The screened able distinguish between germplasms Qinghai-Tibet Plateau those elsewhere. This not only provides reference continued collection but offers scientific basis their conservation utilization.

Language: Английский

Citations

The Genomic Code: the genome instantiates a generative model of the organism DOI

Kevin J. Mitchell,

Nick Cheney

Trends in Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

How does the genome encode form of organism? What is nature this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that encodes a generative model organism. In scheme, analogy with variational autoencoders (VAEs), comprises connectionist network, embodying compressed space 'latent variables', weights get encoded algorithm evolution decoded through processes development. The accounts for complex, distributed genetic architecture most traits emergent robustness evolvability developmental processes, while also offering conception lends itself to formalization.

Language: Английский

Citations

Cryptic variation fuels plant phenotypic change through hierarchical epistasis DOI

Sophia G. Zebell, Carlos Martí‐Gómez, B. P. Fitzgerald

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 25, 2025

Cryptic genetic variants exert minimal or no phenotypic effects alone but have long been hypothesized to form a vast, hidden reservoir of diversity that drives trait evolvability through epistatic interactions. This classical theory has reinvigorated by pan-genome sequencing, which revealed pervasive variation within gene families and regulatory networks, including extensive cis-regulatory changes, duplication, divergence between paralogs. Nevertheless, empirical testing cryptic variation's capacity fuel diversification hindered intractable genetics, limited allelic diversity, inadequate resolution. Here, guided natural engineered in recently evolved paralogous pair, we identified an additional pair redundant trans regulators, establishing network controls tomato inflorescence architecture. By combining coding mutations with series populations segregating for all four genes, systematically constructed collection 216 genotypes spanning the full spectrum complexity quantified branching over 27,000 inflorescences. Analysis resulting high-resolution genotype-phenotype map layer dose-dependent interactions paralog pairs enhances branching, culminating strong, synergistic effects. However, also uncovered unexpected antagonism pairs, where accumulating one progressively diminished other. Our results demonstrate how architecture complex dosage from converge shape space under hierarchical model Given prevalence evolution genomes, propose networks elicits hierarchies interactions, catalyzing bursts change. Keyword: mutations, paralogs, redundancy, cis-regulatory, tomato, inflorescence, network, modeling, epistasis.

Language: Английский

Citations

The Trait Coding Rule in Phenotype Space DOI

Jianguo Wang, Xionglei He

Phenomics, Journal Year: 2025, Volume and Issue: unknown

Published: April 7, 2025

Language: Английский

Citations

Inferring human phenotypes using ancient DNA: from molecules to populations DOI

Manuel Ferrando-Bernal, Colin M. Brand, John A. Capra

et al.

Current Opinion in Genetics & Development, Journal Year: 2024, Volume and Issue: 90, P. 102283 - 102283

Published: Nov. 29, 2024

Language: Английский

Citations

Mutations in the albinism gene oca2 alter vision-dependent prey capture behavior in the Mexican tetra DOI

Stefan Choy,

Sunishka Thakur,

Ellen Polyakov

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 20, 2024

Abstract Understanding the phenotypic consequences of naturally occurring genetic changes, as well their impact on fitness, is fundamental to understanding how organisms adapt an environment. This critical when variants have pleiotropic effects, determining each phenotype impacted by a gene contributes fitness essential understand and why traits evolved. A striking example contributing trait evolution oca2 gene, coding mutations in which underlie albinism reductions sleep blind Mexican cavefish, Astyanax mexicanus . Here, we characterize effects larval prey capture. We find that conspecific surface fish with engineered allele are hunting, they use cave-like, wide angle strikes capture prey. However, unlike cavefish or dark, rely lateral line mediated mutant vision at from angles. Finally, while do not outcompete pigmented siblings albino light. raises possibility detrimental feeding surface-like lighted environment, but does negative for dark environments. Together, these results demonstrate plays role behavior A. Further, expand our evolution.

Language: Английский

Citations

Trehalose mediates salinity-stress tolerance in natural populations of a freshwater crustacean DOI

Joana L. Santos, Fabienne Nick, Nikko Adhitama

et al.

Current Biology, Journal Year: 2024, Volume and Issue: 34(18), P. 4160 - 4169.e7

Published: Aug. 20, 2024

Salinization poses an increasing problem worldwide, threatening freshwater organisms and raising questions about their ability to adapt. We explored the mechanisms enabling a planktonic crustacean tolerate elevated salinity. By gradually water salinity in clonal cultures from 185 Daphnia magna populations, we showed that salt tolerance strongly correlates with native habitat salinity, indicating local adaptation. A genome-wide association study (GWAS) further revealed major effect of Alpha,alpha-trehalose-phosphate synthase (TPS) gene, suggesting trehalose production facilitates tolerance. Salinity-tolerant animals positive correlation between concentrations, while intolerant failed produce trehalose. Animals non-functional TPS generated through CRISPR-Cas9, supported role stress. Our highlights how keystone animal adapts stress using evolutionary mechanism known bacteria, plants, arthropods.

Language: Английский

Citations

KPRR: a novel machine learning approach for effectively capturing nonadditive effects in genomic prediction DOI

Mianyan Li,

T. E. Hall,

David E. MacHugh

et al.

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 26(1)

Published: Nov. 22, 2024

Abstract Nonadditive genetic effects pose significant challenges to traditional genomic selection methods for quantitative traits. Machine learning approaches, particularly kernel-based methods, offer promising solutions overcome these limitations. In this study, we developed a novel machine method, KPRR, which integrated polynomial kernel into ridge regression effectively capture nonadditive effects. The predictive performance and computational efficiency of KPRR were evaluated using six datasets from various species, encompassing total 18 All the traits known be influenced by additive, dominance, or epistatic We compared against other prediction methods: SPVR, BayesB, GBLUP, GEBLUP, GDBLUP, DeepGS. For dominated additive effects, achieved superior accuracies in wheat dataset comparable cattle when GBLUP. dominance matched GDBLUP pig outperformed sheep dataset. exhibiting some traits, while BayesB showed others. Incorporating GBLUP model led overall improvements accuracy. Regarding efficiency, was consistently fastest, slowest. Our findings demonstrated that provided advantages over capturing

Language: Английский

Citations